Measurements of ion concentrations were obtained from synaptic structures in the molecular layer of mouse cerebellar cortex in order to determine physiological changes that occur after neuronal activity. The areas of interest were first characterized by low-dose, dark-field mapping, from which the dry mass content could be determined. Microanalytical data could subsequently be corrected for mass-loss produced by electron beam damage. X-ray spectra, recorded from postsynaptic endoplasmic reticulum (ER) cisterns situated in Purkinje cell dendritic spines, showed two different populations: one with high calcium levels in the ER and low levels in the surrounding cytoplasm, and the other with lower calcium levels in the ER and higher levels in the cytoplasm. Additional analyses were performed on the dendrite mitochondria and ER, as well as on presynaptic terminals and neuroglia.